rtdMerge: Integrate the transcripts in the inference RTD to the...

In wyguo/RTDBox: High resolution Transcriptome using Single Molecule PacBio Iso-seq data

Integrate the transcripts in the inference RTD to the reference RTD.

Usage

rtdMerge(
  inf_file,
  ref_file,
  prefix_ref = "ref",
  prefix_inf = "inf",
  chimeric_tolerance = 0.05,
  data_dir = NULL
)

Arguments

inf_file	The gtf file of a inference RTD,e.g. a RTD assembled from short reads
ref_file	The gtf file of a high confident reference RTD, e.g. a RTD assembled from long reads. The transcripts of the reference RTD will be all kept in the final results.
prefix_ref	A prefix attached to the gene and transcript ids to distinguish their origin of "ref" RTD. Default: "ref"
prefix_inf	A prefix attached to the gene and transcript ids to distinguish their origin of "inf" RTD. Default: "inf"
chimeric_tolerance	Chimeric gene overlap percent, default: 0.05. If the overlap of two gene models < x \item data_dirThe directory to save the results

A merged RTD saved in the data_di Integrate the transcripts in the inference RTD to the reference RTD.

wyguo/RTDBox documentation built on Jan. 31, 2023, 1:19 a.m.